Inhibiting the immune checkpoint (ICP) PD-1 based on PD-L1 expression status has revolutionized the treatment of various cancers, yet its efficacy in anaplastic thyroid carcinoma (ATC) remains limited. The therapeutic response depends upon multiple factors, particularly the conduciveness of the tumor's immune milieu. This study comprehensively evaluated and classified ATC's immune microenvironment (IME) to elucidate the factors behind suboptimal response to anti-PD therapy. Utilizing multiplex-immunofluorescence and immunohistochemistry, we retrospectively analyzed 26 cases of ATC for expression of ICPs PD-L1, PD-1, CTLA4, TIM3, and Galectin-9 and tumor-infiltrating cytotoxic T lymphocytes (CTL)-the effector cells, the anti-tumor NK cells, the immune-inhibitory myeloid-derived suppressor (MDSC) and regulatory T (Treg) cells, and B lymphocytes. Most ATCs (65%) exhibited PD-L1 positivity, but only 31%, in addition, had abundant CTL (type I IME), a combination associated with a better response to ICP inhibition. Additionally, PD-1 expression levels on CTL were low/absent in most cases-a "target-missing" situation-unfavorable for an adequate therapeutic response. All but one ATC showed nuclear Galectin-9 expression. The documentation of nuclear expression of Galectin-9 akin to benign thyroid is a first, and its role in ATC pathobiology needs further elucidation. In addition to less abundant PD-1 expression on CTL, the presence of MDSC, Treg, and exhausted cytotoxic T lymphocytes in the immune milieu of ATC can contribute to anti-PD resistance. TIM3, the most frequently expressed ICP on CTL, followed by CTLA4, provides alternate therapeutic targets in ATC. The co-expression of multiple immune checkpoints is of great interest for ATC since these data also open the avenue for combination therapies.